Forgot to unparent armature while editing mesh, how to fix deformation?
I downloaded your file, the issue is indeed from Shapekeys.
The reason why you can't see them is that you did a word research of your shape keys, and none of them correspond to, so they are hidden. Sympy remove the research and you will get your shape keys displayed :



Then, if you want your modifications to be definitive instead of shape keys, you simply have to select and delete every shape key, keeping the shape you want to keep as the last to delete. Here I did the manipulations to make the Key 2 as definitive shape: